Peter: >>But natural selection can only test a functional feature
already present to some minimal degree. If we consider the entire
historical developmental path of a functionality (e.g. an enzyme),
including all of the functional information contained in it, its
specific activity must have started sometime with a minimal amount of
activity just sufficient to make it selectable. And before that? This is
the interesting part of its history, because without selection, we can
estimate a probability of random emergence. Afterwards, normal darwinian
evolution sets in, and I see no way of estimating probabilities. There
may be many other critical points in the evolution of a new function,
but this is certainly the first one of them - and it is habitually
ignored by evolutionary biologists.<<

David: >Mutated versions of a functional gene may retain the initial
function under some circumstances but change under other conditions.
The classic example of this is temperature sensitivity in mutations. A
change in temperature may directly affect the protein configuration, or
it may induce heat shock, causing chaperone proteins to be put into use
for controlling heat damage and thus freeing the formerly chaperoned
proteins to assume new configurations. Several detrimental examples are
known experimentally. However, Carter et al. (1998, J. Paleont.
72:991-1010) suggested that a low-temperature sensitive mutation in a
protein involved in bivalve shell structure could have mediated changes
from aragonite to calcite. This was based on the paleontological
pattern rather than genetic work.<

Peter: Mutations conditionally activating / desactivating a function
certainly did not produce the information specifying this function, they
just switch its use on or off.
>>The only reason I brought it up at all is because natural selection is the only natural source of biological information we know of. <<

David: >I would think mutation is the source of information and
selection tests the usefulness of the information in a given context.<

Peter: Second half sentence: yes! - first half: no! "Information" has
been used in different ways, but I think in a biological context, it is
most reasonable to use it in the sense of a specification for a
molecular structure required for a specific function. Its meaningful, or
semantic, information content is thus defined by the biological
function. Mutations are random and do not "mean" anything, unless they
are tested by natural selection. They may produce a new structure, but
this structure only carries meaningful biological information with
respect to the effects of natural selection. The concept of random
mutations producing information has led to the very questionable
speculation that meaningful information may spontaneously emerge out of
nothing.

Peter: >>What I call a truly novel gene is one whose function has never
before existed in the entire biosphere, no matter what led to the last
step which originated the first minimal amount of the new activity. If
it is a mixing of old genes, the new gene may display a combination of
the old functions (whose novelty is a matter of definition, but these
cases need not concern us here), or possibly (but very unlikely)
something entirely new, while the old functions no longer exist (perhaps
due to clipping). For a reasonable discussion of such a possibility, we
should have actual examples where this happened.<<

David: >How specifically do you define function? The only way I can
think of to ensure that a gene function has never before appeared in the
biosphere is to look at genes interacting with novel artificial
compounds (resistance to DDT, for example). It seems more feasible and
equally relevant to look at genes that clearly show innovation in a
given organism. The antifreeze gene in the Antarctic toothfish, derived
from trypsinogen, is both structurally and functionally novel (Chen et
al. 1997. PNAS USA 94:3811-3816). Perhaps a similar antifreeze gene
evolved in some organism during one of the Precambrian or Paleozoic ice
ages, but that does not seem to distract from the novelty of this
innovation.<

Peter: You are right in stating that, in general, it will not be
possible to find out whether a given new function has never before
existed. I should have been more careful in asking for actual examples.
In this sense, my concept of a "truly novel gene" is a hypothetical one.
But is an evolution of an entire biosphere at all imaginable without
such cases? But the functional novelty in your examples could be
investigated by trying to find plausible concrete ways of their having
evolved. DDT resistance might have arisen as a concequence of
preexisting enzymes for other substrates already happening to have some
minimal function with rewpect to DDT - but I don't know the case.

Peter: >>This is the reason why I concentrate on folds (i.e. sequences
without any recognizable homology), rather than families.<<

David: >Different folds may have recognizable homology at some other
level. For example, there are two aminoacyl-tRNA synthetase families.
The proteins show no similarity across families. However, the DNA
sequences are similar if you turn one of them around in the opposite
direction (Rodin and Ohno, 1995, Orig. Life Evol. Biosphere
25:565-589). Most of the antifreeze gene mentioned above is
poly-Thr-Ala-Ala, which is unlikely to fold in the same way as the
original protein, although the first exon is retained largely intact.
These codons are derived largely from intronic nucleotides in the
original gene, also involving a frame shift for those parts derived from
previously exonic nucletides. Thus, what was non-functional DNA in the
ancestral gene is now functional.<

Peter: This is an interesting case. However, I suspect that, the
physico-chemical requirements for an antifreeze function may be rather
minimal.

David: >>>>> The example of a pseudogene reactivated, discussed in other
posts, would be a case of passing through unselected "random"
intermediates before arriving at a useful function.<<<<<

Peter: >>>>Do you know of any case where such a path via unselected
intermediates has been documented in a real biological system, not just
stated as a general hypothesis?<<<<

David: >Actually, that was a specific example rather than a general
idea. Gene duplication was promptly followed by one copy becoming a
pseudogene in the ancestor of true ruminants (Pecora). True deer,
giraffes, antelopes, sheep, and early-diverging bovids all have a
pseudogene. However, partial gene conversion in the common ancestor of
certain bovids (cattle, Cape buffalo, and water buffalo) corrected three
major mutations in the pseudogene, allowing it to resume a function
similar to that of the ancestral gene but in a different part of the
body. Most of the gene is still homologous to the pseudogene. This is
certainly not a particularly novel function, but it does show
functionality after a period of unselected mutation.<

Peter: Partial gene conversion (as opposed to three different reverse
mutations) is a lucky one-step change, due to an unequal crossing-over
during DNA replication, whose probability of occurrence might be similar
to that of a lucky single-nucleotide mutation. It doesn't represent a
multi-step mutational random path having non-selected intermediates.

Tim Ikeda: >>>Interestingly, this system arose in much the way that one
would expect an IC system to evolve: indirectly, through steps of
selection under conditions that were not the same as where the system
finally emerged.<<<

Peter: >>If this should turn out to be the case, it would not constitute
an IC system, as each mutation can be selected by itself and the
intermediate is viable.<<

David: >This hinges on the definition of IC [irreducibly complex]. If
it is defined strictly as a multipart system that cannot function when
incomplete and cannot evolve through intermediate steps, then the system
would not be IC. However, the system does pass some of the criteria
proposed as proof that a system is IC. It is a multipart system that
does not function without all its parts, and the partial systems are not
favored by selection. Thus, it might be more accurate to say that this
example shows certain popular criteria for IC are inadequate.<

Peter: I don't think the leading ID people would be satisfied with an IC
definition admitting partial systems "not favored by selection", but
viable. Rather, they would insist that each partial system on any
conceivable evolutionary path would be lethal.